ArticleThe journal of physical chemistry letters2019
Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds.
Article in The journal of physical chemistry letters, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Molecular Periphery Design Allows Control of the New Nitrofurans Antimicrobial Selectivity.Molecules (Basel, Switzerland) · 2024Article
- Structure-basedComputational and structural biotechnology journal · 2021Review
- AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks.International journal of molecular sciences · 2020Article
- Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses.Molecules (Basel, Switzerland) · 2019Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptional repressor EthR from Mycobacterium tuberculosis is a valuable target for antibiotic booster drugs. We previously reported a virtual screening campaign to identify EthR inhibitors for development. Two ligand binding orientations were often proposed, though only the top scoring pose was utilized for filtering of the large data set. We obtained biophysically validated hits, some of which yielded complex crystal structures. In some cases, the crystallized binding mode and top scoring mode agree, while for others an alternate ligand binding orientation was found. In this contribution, we combine rigid docking, molecular dynamics simulations, and the linear interaction energy method to calculate binding free energies and derive relative binding energies for a number of EthR inhibitors in both modes. This strategy allowed us to correctly predict the most favorable orientation. Therefore, this widely applicable approach will be suitable to triage multiple binding modes within EthR and other potential drug targets with similar characteristics.
Identifiers
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Registered trials
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